That is a very hard question to answer as there are so many games with amazing musical scores, especially since the era of CD based consoles and PCs.

Many space based games definitely contain some amazing musical scores. There were music sequences in the online game Earth and Beyond that were truly majestic and captured the sense of floating and moving through the expanses of space very well.

But overall I think it has to be something by Nobuo Uematsu. I cannot give a single title though as most of his music is exceptional and manages to capture emotion so well. Well OK, something from the S Generation album, the "Main theme of FFVII" maybe.